I've get the following error using grompp<br><br>Fatal error: Group Protein_A not found in indexfile.<br>Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp<br><br>********<br>I'm not quite sure what index file it is trying to use, or why is there any problem...
<br>the corresponding .top file:<br><br>[ molecules ]<br>; Compound #mols<br>Protein_A 1<br>Protein_B 1<br>SOL 5417<br> <br>***********<br><br>Corresponding .mdp file:<br><br>tc-grps = Protein_A SOL Protein_B
<br><br>*****<br><br>here's what I do, before I get to the problem:<br>pdb2gmx, editconf, genbox<br>grompp, genion, pdb2gmx<br>grompp, mdrun (energy min)<br>grompp (for PosRes) -> throws the error (this is the 1st time where there is t-coupling)
<br><br>what am I getting wrong?<br><br><br><div><span class="gmail_quote">On 12/21/05, <b class="gmail_sendername">Tamas Horvath</b> <<a href="mailto:hotafin@gmail.com">hotafin@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Yes, I intended to do so (I mean to create physiological K+, Cl- concentrations)<div><span class="e" id="q_1084e82b3ae63218_1"><br><br><div><span class="gmail_quote">On 12/21/05, <b class="gmail_sendername">Christian Burisch
</b> <<a href="mailto:burisch@bph.rub.de" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
burisch@bph.rub.de</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Tamas Horvath wrote:<br><br>Hi all,<br><br>> Of course I can, but the only way to do that is to capture the pdb2gmx or
<br>> grompp output as it seems...<br><br>it is also in the itp/top-File!<br><br>grep qtot protein.itp | tail -n 1<br><br>and then proceed with awk or perl or something like that.<br>Perhaps you should not only neutralise the system, but rather create a
<br>physiological ion concentration (which you can calculate of course<br>from the system charge and the number of SOL molecules).<br><br>HTH<br><br>Christian<br><br>_______________________________________________<br>gmx-users mailing list
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